13 research outputs found
Raw juice extraction from sugar cane and sugar beet
No full textDocument uit de collectie Chemische ProcestechnologieDelftChemTechApplied Science
Judges and lawmaking at the International Criminal Tribunals for the former Yugoslavia and Rwanda
No full textIn this study the author examines the question of whether the judges at the International Criminal Tribunals for the former Yugoslavia and Rwanda are entitled to make law. Instances of substantive and procedural lawmaking at the tribunals are analysed. The context within which tribunal law is made and the institutional culture at the tribunals are discussed. The author examines the influence of the principle of legality in distinguishing between legitimate and illegitimate exercises of the lawmaking power of tribunal judgesUBL - phd migration 201
Active personality and non-extradition of nationals in international criminal law at the dawn of the twenty-first century : adapting key functions of nationality to the requirements of International Criminal Justice
No full textIn the era of international(ized) criminal courts and tribunals, classical concepts of international criminal law such as principles and rules of extradition and of extraterritorial jurisdiction have fallen into oblivion. At the same time, globalization and the establishment of international criminal jurisdictions have brought about fundamental changes of relevant attributes of the international system, justifying and necessitating renewed scholarly attention for these seemingly over-analyzed phenomena. Due in major part to these systemic changes, the non-extradition of nationals increasingly comes under fire. As a consequence, several attempts were undertaken in recent years to disallow or at least considerably limit it. Focusing on two such endeavors (under the European Arrest Warrant and in the context of the International Criminal Court), this study attempts to identify the status and the role of the non-extradition of nationals and of its counterpart, the active personality principle in international (criminal) law. Recognizing that the non-extradition of nationals cannot be easily discard, in theory or in practice, the author considers ways to adapt these long-standing features of international cooperation in criminal matters to the requirements of international criminal justice.LEI Universiteit LeidenFDR Sovereignty, International Governance and Global Values -- ou
Localization of an accessory helicase at the replisome is critical in sustaining efficient genome duplication
No full text© The Author(s) 2010. Published by Oxford University PressGenome duplication requires accessory helicases to displace proteins ahead of advancing replication forks. Escherichia coli contains three helicases, Rep, UvrD and DinG, that might promote replication of protein-bound DNA. One of these helicases, Rep, also interacts with the replicative helicase DnaB. We demonstrate that Rep is the only putative accessory helicase whose absence results in an increased chromosome duplication time. We show also that the interaction between Rep and DnaB is required for Rep to maintain rapid genome duplication. Furthermore, this Rep–DnaB interaction is critical in minimizing the need for both recombinational processing of blocked replication forks and replisome reassembly, indicating that colocalization of Rep and DnaB minimizes stalling and subsequent inactivation of replication forks. These data indicate that E. coli contains only one helicase that acts as an accessory motor at the fork in wild-type cells, that such an activity is critical for the maintenance of rapid genome duplication and that colocalization with the replisome is crucial for this function. Given that the only other characterized accessory motor, Saccharomyces cerevisiae Rrm3p, associates physically with the replisome, our demonstration of the functional importance of such an association indicates that colocalization may be a conserved feature of accessory replicative motors.Biotechnology and Biological Sciences Research Council (BB/G005915/1 and BB/E0020690 to P.M.); MRC (G0800970 to R.G.L.); Leverhulme Trust (to C.J.R.). Funding for open access charge: BBSRC
Clearing transcription barriers to replication
No full textSupplementary Data are available at NAR Online at https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz170#supplementary-data .Copyright © The Author(s) 2019. Bacterial genome duplication and transcription require simultaneous access to the same DNA template. Conflicts between the replisome and transcription machinery can lead to interruption of DNA replication and loss of genome stability. Pausing, stalling and backtracking of transcribing RNA polymerases add to this problem and present barriers to replisomes. Accessory helicases promote fork movement through nucleoprotein barriers and exist in viruses, bacteria and eukaryotes. Here, we show that stalled Escherichia coli transcription elongation complexes block reconstituted replisomes. This physiologically relevant block can be alleviated by the accessory helicase Rep or UvrD, resulting in the formation of full-length replication products. Accessory helicase action during replication-transcription collisions therefore promotes continued replication without leaving gaps in the DNA. In contrast, DinG does not promote replisome movement through stalled transcription complexes in vitro. However, our data demonstrate that DinG operates indirectly in vivo to reduce conflicts between replication and transcription. These results suggest that Rep and UvrD helicases operate on DNA at the replication fork whereas DinG helicase acts via a different mechanism.UK Biotechnology and Biological Sciences Research Council (BBSRC) [BB/I001859/2, BB/N014863/1 to P.M., BB/K015729/1, BB/N014995/1 to C.J.R. and BB/I003142/1 to N.J.S. and M.S.D.]. Funding for open access charge: York Open Access Fund
Cas1-Cas2 physically and functionally interacts with DnaK to modulate CRISPR Adaptation
No full textData Availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD042090.Supplementary Data are available at NAR Online https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkad473#supplementary-data .Copyright © The Author(s) 2023. Prokaryotic Cas1–Cas2 protein complexes generate adaptive immunity to mobile genetic elements (MGEs), by capture and integration of MGE DNA in to CRISPR sites. De novo immunity relies on naive adaptation—Cas1–Cas2 targeting of MGE DNA without the aid of pre-existing immunity ‘interference’ complexes—by mechanisms that are not clear. Using E. coli we show that the chaperone DnaK inhibits DNA binding and integration by Cas1–Cas2, and inhibits naive adaptation in cells that results from chromosomal self-targeting. Inhibition of naive adaptation was reversed by deleting DnaK from cells, by mutation of the DnaK substrate binding domain, and by expression of an MGE (phage λ) protein. We also imaged fluorescently labelled Cas1 in living cells, observing that Cas1 foci depend on active DNA replication, and are much increased in frequency in cells lacking DnaK. We discuss a model in which DnaK provides a mechanism for restraining naive adaptation from DNA self-targeting, until DnaK is triggered to release Cas1–Cas2 to target MGE DNA.The BBSRC [BB/T006625-1 to E.L.B., BB/T007168/1 to C.J.R.]; Croatian Science Foundation [IP-2016-06-8861 to I.I.B.]. Funding for open access charge: University of Nottingham Gold
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
No full textThe Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].This work was supported by grants from a graduate student research award from the Society of Systematic Biologists and the University of Kentucky G.F. Ribble Endowment (to P.M.H.), by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/BEX 2806/09-6 to P.L.V.P.), and by the National Science Foundation (DEB-0949532 and DEB-1355000 to D.W.W., DEB-1120516 to E.M.L., IIP-1313554 to A.R.L. and E.M.L, DEB-1355071 to J.M.B., DEB-1441719 to R.A.P., DEB-1311442 to P.L.V.P., DEB-1354506 to R.C.T., DEB-1021247 to E.P. and C.J.R., DEB-1021299 to K.M. Kjer, and DEB-1257610, DEB-0641023, DEB-0423286, and DEB-9984496 to C.J.R.), and the Australian Research Council (DP120104146 to J.S.K. and S.C.D.). S.R.R. thanks SENESCYT (Arca de Noé Initiative; SRR and O. Torres-Carvajal principal investigators) for funding for tissue collection. J.L. was supported by the Systematics Association and the Linnean Society Systematics Research Fund. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program (DGE-3048109801 to P.M.H.) and by the National Science Foundation-supported National Center for Supercomputing Applications Blue Waters Graduate Research Fellowship Program (under Grant No. 0725070, subaward 15836, to P.M.H.). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation
A study of breakwater gap wave diffraction using close range photogrammetry and finite and infinite elements.
No full textIn this thesis the diffraction of water waves passing through a gap in a breakwater is investigated experimentally, using close range photogrammetry, and numerically, using finite and infinite elements. The author was particularly interested in validating specific breakwater gap diffraction diagrams given in popular coastal engineering design manuals. Breakwater gap configurations with the following gap width to wave length ratios (B/L ratios) were analysed, both experimentally and numerically, namely: B/L = 1,64; 1,41; 1,2; 1; 0,75; 0,5. These configurations are symmetrical, i.e. both breakwater arms lie on the same straight line. An asymmetrical B/L = 1,64 breakwater gap configuration was also analysed. Previous experimental breakwater gap diffraction investigations are reviewed leading to the conclusion that the reported results are inconclusive due to (1) the relatively poor accuracy with which the wave heights were measured and (2) secondary basin effects which were superimposed upon and thus distorted the pure diffraction phenomena. In the experimental breakwater gap configurations investigated by the author, splitter plates were used to eliminate the reflection problems on the seaward side of the breakwaters, whilst a novel photogrammetric wave height measurement technique was used to measure accurately the wave heights in the entire basin, before they could be distorted by reflecting waves, basin resonance effects, etc. This "infinite basin technique" was used to simulate experimentally and measure the diffraction of a continuous wave train entering an infinite basin via a gap in an approximate totally absorbing breakwater. A number of different photogrammetric wave height measurement techniques based on analogue procedures, the theory of projective transformations, and the theory of the deformed reference plane, are investigated and developed. It was found that the technique based on the projective transformation theory, and in which the plates are analysed using a stereo-comparator linked to a microcomputer, is the most accurate. Using this technique it was found that, with the cameras situated approximately 5 m above the water surface, the wave heights in the basin can be measured with an accuracy of better than 2 mm. The above method, in conjunction with the infinite basin technique, was used to analyse the experimental breakwater gap configurations. The basic linear wave theory is described leading to the derivation of the Helmholtz diffraction equation. The classical diffraction theories for the semi-infinite breakwater and breakwater gap configurations are reviewed and compared. The Better-off refraction - diffraction equation is then briefly derived. A review of previous numerical refraction - diffraction investigations, and also of modern numerical methods for water wave diffraction and refraction-diffraction, is given. This review led to the adoption of the finite and infinite element program "WAVE", developed at the University College of Swansea, to model numerically the experimental breakwater gap configurations. The use of the "WAVE" program to model breakwater gap wave diffraction is novel and certain conceptual problems had to be overcome. Finally, the experimental and numerical diffraction diagrams obtained were compared to analytical diagrams where these were available. The correlation between the finite element and analytical results is excellent. When comparing the experimental and finite element results the general conclusions are : 1) in regions outside the shadow zones the linear diffraction theory is conservative except close to small gaps (B/L ≤ 1); and 2) within the shadow zones the linear theory is not conservative and one will have to allow for non-linear effects such as radiating second-order waves generated at the breakwater tips, and increased wave orthogonal spreading near the gap centre line and subsequent orthogonal bunching in the shadow zones caused by wave steepness differences along the crests. Other conclusions drawn are : 1) the photogrammetric techniques described are the best available for the experimental simulation and analysis of infinite domain diffraction and refraction - diffraction problems; and 2) the finite and infinite element program "WAVE" is a very useful tool for the prediction of wave heights in large harbour basins
Toenail selenium status and the risk of Barrett’s esophagus: the Netherlands Cohort Study
No full textObjective: To investigate the association between selenium and the risk of Barrett's esophagus (BE), the precursor lesion of esophageal adenocarcinoma. Methods: Data from the prospective Netherlands Cohort Study were used. This cohort study was initiated in 1986, when 120,852 subjects aged 55-69 years completed a questionnaire on dietary habits and lifestyle, and provided toenail clippings for the determination of baseline selenium status. After 16.3 years of follow-up, 253 BE cases (identified through linkage with the nationwide Dutch pathology registry) and 2,039 subcohort members were available for case-cohort analysis. Cox proportional hazards models were used to calculate incidence rate ratios (RR). Results: The multivariable-adjusted RR for the highest versus the lowest quartile of toenail selenium was 1.06 (95% CI 0.71-1.57). No dose-response trend was seen (p trend = 0.99). No association was found in subgroups defined by sex, smoking status, body mass index (BMI), or intake of antioxidants. For BE cases that later progressed to high-grade dysplasia or adenocarcinoma, the RR for a selenium level above the median vs. below the median was 0.64 (95% CI 0.24-1.76). Conclusions: In this large prospective cohort study, we found no evidence of an association between selenium and risk of BE. © 2010 The Author(s)
Taxonomy and phylogeny of the genus Mycosphaerella and its anamorphs
No full textHistorically plant pathogenic species of Mycosphaerella have been regarded as host-specific, though this hypothesys has proven difficult to test largely due to the inavailability of fungal cultures. During the course of the past 20 years a concerted effort has been made to collect these fungi, and devise methods to cultivate them. Based on subsequent DNA sequence analyses the majority of these species were revealed to be host-specific, though some were not, suggesting that no general rule can be applied. Furthermore, analysis of recent molecular data revealed Mycosphaerella to be poly- and paraphyletic. Teleomorph morphology was shown to be too narrowly defined in some cases, and again too widely in others. Mycosphaerella and Teratosphaeria as presently circumscribed represent numerous different genera, many of which can be recognised based on the morphology of their 30 odd associated anamorph genera. Although Mycosphaerella is generally accepted to represent one of the largest genera of ascomycetous fungi, these data suggest that this is incorrect, and that Mycosphaerella should be restricted to taxa linked to Ramularia anamorphs. Furthermore, other anamorph form genera with Mycosphaerella-like teleomorphs appear to represent genera in their own right
